OBJECTIVE Gut or genital mucosa tissue specimens were collected from rhesus macaques before and after immunization or virus infection. Samples were processed to preparation of mRNA and PCR-based assays were used to quantify the levels of individual T cell receptor genes expressed in these samples. Further analysis of the mRNA population was accomplished by spectrotyping analysis, wherein individual T cell receptor expressing families are distinguished on the basis of the size distribution of expressed genes. Spectrotyping analysis provides additional information about the specificity for each population and the changes occurring after infection or immunization. Retrovirus infection of macaques caused a rapid and extensive shift in the population of T cells expressing the Vgamma9 T cell receptor gene. These changes were larger than what was observed after immunization, though both were significantly different from control specimens. Similar studies done on residual uterine samples from women patients, showed a distribution of Vgamma9 T cell receptor expression that was similar to uninfected macaques. FUTURE DIRECTIONS We are expanding the panel of probes to examine additional Vdelta and Vgamma sequences and we are improving conditions for studying Vbeta gene expression. In addition, further work is necessary to improve sampling and sample handling procedures. All of these efforts are directed to gaining better understanding of lymphocyte populations present in the gut and genital mucosa. KEY WORDS AIDS, mucosa, immunology, T cell receptor FUNDING NIH R01 AI/RR42534